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Yorodumi- PDB-6yax: Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yax | ||||||
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Title | Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CD32 CD32b Fc gamma receptor Fc gamma receptor II b Fab Complex | ||||||
Function / homology | Function and homology information IgG binding / regulation of immune response / transmembrane signaling receptor activity / cell surface receptor signaling pathway / immune response / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fisher, H. / Tews, I. / Orr, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05) Authors: Fisher, H. / Tews, I. / Orr, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yax.cif.gz | 403 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yax.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/6yax ftp://data.pdbj.org/pub/pdb/validation_reports/ya/6yax | HTTPS FTP |
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-Related structure data
Related structure data | 5occS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AAABBB
#3: Protein | Mass: 20455.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2C, CD32, FCG2, IGFR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P31995 |
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-Antibody , 2 types, 4 molecules HHHIIIMMMLLL
#1: Antibody | Mass: 23210.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 22979.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 280 molecules
#5: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2- propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1.0 M tris (base), BICINE, 40% v/v PEG 500 MME, 20% w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.86 Å / Num. obs: 41024 / % possible obs: 99.3 % / Redundancy: 7.2 % / CC1/2: 0.995 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→2.87 Å / Num. unique obs: 3003 / CC1/2: 0.491 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OCC Resolution: 2.8→47.86 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: FREE R-VALUE / ESU R: 0.927 / ESU R Free: 0.355 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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